Morpho: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-08-10T16:07:14ZEcoinformatics Redmine
Redmine Bug #7205 (New): IDs mishandled when an update is made to a package with a DOIhttps://projects.ecoinformatics.org/ecoinfo/issues/72052017-08-10T16:07:14ZJeanette Clark
<p>From a user:</p>
<p>"Hi Julien, sorry to bother you again but I have one more question. I’m<br />trying to update my data sets to include the DOI for the accompanying<br />article (it’s not out yet but I just got the DOI). For one of my data sets<br />I mistakenly hit “publish with DOI” and now I can’t edit / update the<br />record at all either online or via morpho:</p>
<p><a class="external" href="https://knb.ecoinformatics.org/#view/doi:10.5063/F12Z13MD">https://knb.ecoinformatics.org/#view/doi:10.5063/F12Z13MD</a></p>
<p>Online it says I don’t have access, in morpho I get this error:</p>
<p>"Problem with saving to metacat in EML200DataPackage! <?xmlversion = "1.0"><error>Could not write file: /var/metacat/documents/doi:10.5063/F12Z13MD.2: /var/metacat/documents/doi:10.5063/F12Z13MD.2 (No such file or directory)</error></p>
<p>Any tips on how I can fix this and update the record to include the DOI?"</p>
<p>It seems like the user accidentally applied a DOI and then tried to go back to Morpho to edit the package, where it tried to write the new identifier as the DOI.2</p>
<p>The user's problem has been remedied but it seems like this behavior should be fixed</p> Bug #7175 (New): The link for non-numeric attribute domains doesn't work on the exported eml filehttps://projects.ecoinformatics.org/ecoinfo/issues/71752017-03-21T16:32:28ZJing Taotao@nceas.ucsb.edu
<p>To Whom It May Concern:</p>
<p>I am trying to use Morpho to create metadata for a project (Morpho has been updated to the latest version). I have entered all the information (that I have at this time, at least) into Morpho and can view everything that I’ve entered within the software. When I export the metadata and view the html or pdf files, everything is great except with defining nominal codes. For these attributes, a link name “Domain Info” is provided and when clicked the link either returns to the top of the metadata file (clicked within the Morpho preview) or opens a browser window that says “No file exists at the address “/metacat” (clicked from html or pdf files). I have attached a file for example. I am not a coder and have not been able to figure out a way for the nominal/category codes to be listed directly in the metadata export files. I don’t like the thought of having to export all my work from Morpho into Metavist, so thought I’d check with KNB for a possible solution first.</p>
<p>Thanks for any guidance that you are able to provide.</p>
<p>Best,</p>
<p>Jayne</p>
<p>I looked at the html of page and it shows:<br /><td class="innercoleven" align="center" colspan="2"><a href="/metacat?action=read&qformat=export&sessionid=&docid=&displaymodule=attributedomain&entitytype=dataTable&entityindex=4&attributeindex=6"><b>Domain Info</b></a></td></p>
<p>The link looks like to use the metacat read action to read the attributedomain module. However, this link as imported html can't work since it can't have the complete metacat url. I also search the Metacat code and can't find it supporting to display the attribute domain.</p>
<p>I also looked at the eml xslt code. Here is the code to generate the link at the template attributenonnumericdomaincommon:<br /> <a><xsl:attribute name="href"><xsl:value-of select="$tripleURI"/><xsl:value-of select="$docid"/>&displaymodule=attributedomain&entitytype=<xsl:value-of select="$entitytype"/>&entityindex=<xsl:value-of select="$entityindex"/>&attributeindex=<xsl:value-of select="$attributeindex"/></xsl:attribute></p>
<p>It seems there are issues on the export feature of Morpho. So the link doesn't work. However, we have a way to work around the issues. First, you may save the package to a Metacat server from Morpho. Then you can open the package on the link from a browser. You may save the html file which shows up on your browser to replace the metadata.html on your exported package directory.</p>
<p>Here is the link of an eml on our KNB web site (which is our default Metacat server on Morpho):<br /><a class="external" href="https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=default&amp;displaymodule=printall">https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=default&amp;displaymodule=printall</a><br />When you click the link "Domain info", it will show up the information. After you save your eml into KNB, you can open your package by modifying the above link - replace "autogen.2017031514432105092.2" by your docid.</p>
<p>If you do want to use one html to show all the information, you may use this link:<br /><a class="external" href="https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=metacatui&amp;displaymodule=printall">https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=metacatui&amp;displaymodule=printall</a><br />As I said, when you try to open your eml, you need to replace the "autogen.2017031514432105092.2" by your docid.</p> Bug #6846 (New): Morpho hangs when exporting data packagehttps://projects.ecoinformatics.org/ecoinfo/issues/68462015-09-25T17:33:14ZBryce Mecummecum@nceas.ucsb.edu
<p>I was able to hang Morpho sometimes when exporting a newly-created data package.</p>
<p>Summary of my environment:<br />- OS: Mac OS X 10.10.5<br />- JRE: 1.8.0_51-b16<br />- Morpho: 1.11.0</p>
<p>Steps to reproduce:<br />- Open Morpho (Mac application form of it, launched via the Finder)<br />- Click File > Create new data package<br />- Enter information for 'Title', 'Owner', 'Contact', hitting next and accepting defaults for all other fields.<br />- Click Finish in the new data package wizard<br />- Save the data package using File > Save, and leave 'Save Locally" checked and click "Save" <br />- Attempt to export the package using File > Export, leave 'Export to a Directory' selected and click 'Export'<br />- Observe that the program is now hung.</p>
<p>The last step sometimes works and sometimes doesn't. I haven't determined what I'm doing that makes it hang sometimes and not other times.</p> Bug #6745 (New): Morpho main window doesn't look good in windows 8https://projects.ecoinformatics.org/ecoinfo/issues/67452015-05-04T17:15:30ZJing Taotao@nceas.ucsb.edu
<p>Margaret reported the morpho main window doesn't look good in windows 8. However, Jing didn't see the issue when he ran windows 8-1 in VirtualBox.</p> Bug #6544 (New): Check the validity of the URL before letting someone save it.https://projects.ecoinformatics.org/ecoinfo/issues/65442014-04-30T00:14:43ZJing Taotao@nceas.ucsb.edu
<p>Corinna found that the morpho hangs if the metacat url is set incorrectly. But I can't reproduce it. If the url missed a "metacat" ( see using <a class="external" href="https://poseidon.limnology.wisc.edu/metacat">https://poseidon.limnology.wisc.edu/metacat</a> rather than <a class="external" href="https://poseidon.limnology.wisc.edu/metacat/metacat">https://poseidon.limnology.wisc.edu/metacat/metacat</a>), morpho is still responsive. But the login takes for ever.</p>
<p>No matter what behavior it is, we need to check the the validity of the URL.</p> Bug #6500 (New): Give users ability to import certifates into Morpho easilyhttps://projects.ecoinformatics.org/ecoinfo/issues/65002014-04-05T00:52:36ZJing Taotao@nceas.ucsb.edu
<p>We may create a ~/.morpho/certs directory and have a simple UI for users to drop certificates to the directory.</p>
<p>On startup, morpho looks in that dir and adds any CA certs it finds to the keystore, and keeps track of them, so if the user removes one then it removes it from the truststore on next restart.</p>
<p>The d1_libclient already has some features. The d1_libclient does this all dynamically at runtime - it does not actually write entries to the trustore, just merges them for runtime use</p> Bug #6410 (New): The box selection of Geographic Coverage screen doesn't work https://projects.ecoinformatics.org/ecoinfo/issues/64102014-02-06T18:36:48ZJing Taotao@nceas.ucsb.edu
<p>Hi Ben,</p>
<p>OK, got it!</p>
<p>One other issue that you may or may not be aware of: in the Geographic<br />Coverage section you can choose box or point methods. Regardless of whether<br />I choose box or point, it only allows me to put in points. So even if I put<br />in four coordinates for bounding a location, it automatically fills in the<br />other boxes (e.g. I put in 38.32 N and the box below is filled in with the<br />same coordinates; when I try to alter it to be the southern boundary, it<br />then changes the northern boundary in the box above; however, in the<br />metadata, it identifies the coordinates of the box as N, S, E, and W, even<br />though it only lets me enter N and W coordinates in the box).</p>
<p>Thank you for your help!</p>
<p><strong>~ Kristina</strong></p>
<p>Kristina Wolf<br />Restoration Ecology Lab<br />Ph.D. Student, Graduate Group in Ecology<br />Department of Plant Sciences<br />B.S. Animal Science, M.S. Soil Science<br />(530) 750-9771</p> Bug #4628 (New): Testing version 1.7.1 beta: Morpho Tree Editor produces invalid documentshttps://projects.ecoinformatics.org/ecoinfo/issues/46282009-12-14T20:56:10ZRick Reevesreeves@nceas.ucsb.edu
<p>Condition: I am using the Morpho Tree Editor to edit the columns in an attribute table. The table was, incidentally, imported into an existing Data Package (originally, nceas.906.5) using the 'Import MS Access Database' utility.</p>
<p>Here are the steps that I took:<br />Click Green Edit button, wait about 45 seconds for the Morpho Editor to <br />appear. I am editing column attributes by clicking each attribute in the 'tree', changing the value, and then clicking on the next attribute. This is a very efficient way to edit multiple table columns/attributes. Once I have modified all of the attributes, and am ready to save them, I click the OK button. Sometimes, the editor window closes and the modifications appear in the attribute table display (on the right side of the screen).</p>
<p>But several times, when I click OK, the Morpho editor screen freezes<br />and the first of the attached messages displays. Trying to recover from the error, I click the 'X' box in the upper right corner of the screen.When I click<br />to close the window (URC), the screen goes away and the second message<br />appears. My changes to the table metadata do not appear, and have been lost.</p>
<p>Note: the alternative method of editing column metadata, the Edit Column Documentation option, requires more mouse clicks and about 25 % more time <br />to use for a given group of attribute edits. this is because of the delay (of several seconds) between the time that the user clicks the mouse on an attribute column and the time that the selection 'registers' on the screen so that the user<br />can edit the field.) And I have some evidence that even using this method to edit columns, sometimes the attribute edits are not saved to the table.</p>
<p>Because of these defects, it takes a very long time to edit large groups of column attributes on stored tables in Morpho. The defects make it difficult to do error-free edition of column attributes. I think that many would-be Morpho users will become frustrated with this performance and resist using the software.</p> Bug #3476 (New): Search Result Selection list elements change when selectedhttps://projects.ecoinformatics.org/ecoinfo/issues/34762008-08-26T22:33:40ZRick Reevesreeves@nceas.ucsb.edu
<p>Intermittent software 'lockup' (approx 50 % of attempts results in the condition):</p>
<p>Occurs on Ubuntu 7.10 platform, JRE 1.5.0.13, Morpho 1.6.1 -</p>
<p>To re-create:</p>
<p>1) Start Morpho (from command line) and log in<br />2) Search Network and Local, All, search string: 'NCEAS 2017'<br />3) From search results, select (double click) DocumentID chadden.48.2 <br /> for viewing.<br />4) Here is what happens: When I select the item, it immediately changes<br /> to another item in the list (e.g., to the entry for DocID nceas.149.17)<br />5) When this happens, the list 'locks up', and selections can not be made.</p>
<p>Again, this only happens about 50 % of the time, and only on Ubuntu (so far).</p> Bug #2216 (New): Custom units not assigned to unit type category properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/22162005-09-30T19:47:27ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>If you create a custom unit that belongs to an existing unit type that contains<br />a space in the name ("Areal Mass Density", "Catalytic Activity", etc) the unit<br />does not subsequently get displayed as a member of that unit type in the NDTW.<br />Instead, when you try to select the unit again for another attribute, it is<br />listed as a unit in a separate unit type ("Arealmassdensity" instead of "Areal<br />Mass Density"). I think it's just a display issue, as the unit is listed in the<br />proper unit type if the DP is closed and re-opened.</p> Bug #2213 (New): "Show all" Morpho editor handles coverage incorrectly depending on orderhttps://projects.ecoinformatics.org/ecoinfo/issues/22132005-09-30T19:37:39ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>If coverage elements in an EML document are listed in an order other than the<br />order used by the DPW (geographicCoverage, temporalCoverage, then<br />taxonomicCoverage), the "Show all" function in the Morpho editor works<br />incorrectly. Extra empty geographic, temporal, and/or taxonomic coverage nodes<br />are added. Some of these extra nodes are inserted checked, others not. I<br />believe this may be the same as bug 1668.</p> Bug #2209 (New): Run the parser when a Save event is generatedhttps://projects.ecoinformatics.org/ecoinfo/issues/22092005-09-28T19:40:18ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>From Bug# 1622:</p>
<p>------- Additional Comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: MCAT won't build under IRIX with Oracle 8.0.5 (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/6">#6</a> From Matt Jones 2004-07-23 08:54 -------</p>
<p>And Sid, in fixing this I think what we should be doing is running the eml<br />parser on the document when a Save event is detected. If the validation fails,<br />we should at a minimum provide an understandable list of the places where more<br />metadata is needed, but even better guide them to those locations so that they<br />can fix them quickly and easily.</p> Bug #2042 (In Progress): Failure when using dataTable, spatialRaster, and spatialVector in tree e...https://projects.ecoinformatics.org/ecoinfo/issues/20422005-03-11T22:53:59ZVeronique Connollyconnolly@nceas.ucsb.edu
<p>Creating metadata using the dataTable, spatialRaster, and spatialVector modules<br />in the Morpho Editor results in an error message and a lost of the information<br />entered in the editor:</p>
<p>I created a simple data package in Morpho using the DPWizard (I only filled in<br />the required fields). Then I opened the tree editor. I clicked on “Show All”<br />and then expanded the dataTable module and entered info for the required fields.<br />I made sure only one SEQUENCE radio button was selected whenever there was a<br />CHOICE (see bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: Radio buttons for choice are "all" set as default in Tree Editor (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1712">#1712</a>). I clicked on “Trim” and then made sure the<br />spatialRaster and spatialVector boxes were not checked. I clicked OK on the<br />Morpho editor. I got the following message:</p>
<p>"The saved document is not valid EML2 for some reason. You can save it <br />locally and fix the problem later, but you will be unable to submit it <br />to the network storage system. Do you want to Continue Exiting the Editor?"</p>
<p>I clicked Yes to that message and then got a message saying "physicalList null" <br />message. I then clicked OK (it takes 4 clicks) to that message and got another<br />error message: “Exception in converting edited XML to DOM!null.”</p>
<p>After I clicked OK for this last message, the dp window was grey (empty) and the<br />butterfly continuously beat its wings, and I had to close the dp. The info I<br />entered in the tree editor was lost. I had saved the dp before I went into the<br />tree editor, but if you don't, you also loose what you had entered in the DPW.</p>
<p>Laura Downey discovered this bug using the spatialRaster module. I tried<br />replicating what I described above using the spatialRaster module and got the<br />same result (I made sure the dataTable and spatialVector boxes were not<br />selected): error messages and lost of info.</p>
<p>I also tried this with the spatialVector, got the first message mentioned above,<br />and then got a message saying “Unable to display this data. However, an empty<br />table with the column header information will be shown.” The info I entered in<br />the editor was then displayed in the data package (data table and table<br />documentation panels). However, this only happened once. After that time, I<br />repeated this process several times in the spatialVector (trying to repeat what<br />I did the first time) and got the same error messages and lost of info described<br />above for the dataTable and spatialRaster modules.</p> Bug #1702 (New): spatial search is not savedhttps://projects.ecoinformatics.org/ecoinfo/issues/17022004-09-28T23:47:07ZChad Berkleyberkley@nceas.ucsb.edu
<p>when you revise a search that you have just performed, the spatial bounding box<br />is reset to the default instead of being left in the state that you left it. <br />When opening a saved search or revising an existing search, the bounding box<br />should retain its position.</p> Bug #1651 (New): Scale requestshttps://projects.ecoinformatics.org/ecoinfo/issues/16512004-08-01T22:29:04ZRobert Washington-Allenwashingtonra@mac.com
<p>In the beginning of Mopho data entries for study scales you have requests for <br />geographic extent and temporal extent. The Temporal extent request does not <br />account for studies that occurr on hour, minute or second scales which will be <br />the case for sudies of high temporal frequency, genomic and microbiological <br />studies. Further you are requesting scale information and scale is both grain <br />(the smallest spatial unit of measure or time step) or extent(the bounds, what <br />you required).</p>